Cite this paper:
Ruoyu LIU, Jun LIU, Haibin ZHANG. Positive selection analysis reveals the deep-sea adaptation of a hadal sea cucumber (Paelopatides sp.) to the Mariana Trench[J]. Journal of Oceanology and Limnology, 2021, 39(1): 266-281

Positive selection analysis reveals the deep-sea adaptation of a hadal sea cucumber (Paelopatides sp.) to the Mariana Trench

Ruoyu LIU1,2, Jun LIU1, Haibin ZHANG1
1 Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China;
2 University of Chinese Academy of Sciences, Beijing 100049, China
Abstract:
The Mariana Trench, the deepest trench on the earth, is ideal for deep-sea adaptation research due to its unique characters, such as the highest hydrostatic pressure on the Earth, constant ice-cold temperature, and eternal darkness. In this study, tissues of a the hadal holothurian (Paelopatides sp.) were fixed with RNA later in situ at ~6 501-m depth in the Mariana Trench, which, to our knowledge, is the deepest in-situ fixed animal sample. A high-quality transcript was obtained by de-novo transcriptome assembly. A maximum likelihood tree was constructed based on the single copy orthologs across nine species with their available omics data. To investigate deep-sea adaptation, 113 positively selected genes (PSGs) were identified in Paelopatides sp. Some PSGs such as microphthalmia-associated transcription factor (MITF) may contribute to the distinct phenotype of Paelopatides sp., including its translucent white body and degenerated ossicles. At least eight PSGs (transcription factor 7-like 2[TCF7L2], ETS-related transcription factor Elf-2-like [ELF2], PERQ amino acid-rich with GYF domain-containing protein[GIGYF], cytochrome c oxidase subunit 7a,[COX7A], type I thyroxine 5'-deiodinase[DIO1], translation factor GUF1[GUF1], SWI/SNF related-matrix-associated actin-dependent regulator of chromatin subfamily C and subfamily E, member 1[SMARCC] and[SMARCE1]) might be related to cold adaptation. In addition, at least nine PSGs (cell cycle checkpoint control protein[RAD9A], replication factor A3[RPA3], DNA-directed RNA polymerases I/Ⅱ/Ⅲ subunit RPABC1[POLR2E], putative TAR DNA-binding protein 43 isoform X2[TARDBP], ribonucleoside-diphosphate reductase subunit M1[RRM1], putative serine/threonine-protein kinase [SMG1], transcriptional regulator[ATRX], alkylated DNA repair protein alkB homolog 6[ALKBH6], and PLAC8 motif-containing protein[PLAC8]) may facilitate the repair of DNA damage induced by the high hydrostatic pressure, coldness, and high concentration of cadmium in the upper Mariana Trench.
Key words:    sea cucumber|Mariana Trench|deep-sea adaptation|positive selection analysis|translucent white body|ossicle degeneration   
Received: 2020-06-23   Revised: 2020-07-27
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